repet
Table of Content
About
The REPET package is a package integrating bioinformatics programs in order to tackle biological issues at the genomic scale. REPET consists in two main pipelines, TEdenovo and TEannot, which are dedicated to the detection, annotation and analysis of repeats in genomic sequences. These pipelines are specifically designed for transposable elements (TEs) detection and annotation.
- TEdenovo - this pipeline starts by comparing the genome with itself using BLASTER. Then it clusters matches with GROUPER, RECON and PILER, programs specific for interspersed repeats. For each cluster, it builds a multiple alignment from which a consensus sequence is derived. Finally these consensus are classified according to TE features and redundant consensus are removed. At the end we obtain a library of classified, non-redundant consensus sequences.
- TEannot - this pipeline mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, using BLASTER, RepeatMasker and CENSOR. An empirical statistical filter is applied to discard false-positive matches. Short simple repeats (SSRs) are annotated along the way with TRF, RepeatMasker and MREPS. Then, MATCHER, via dynamic programming, chains TE fragments belonging to the same, disrupted copy. A "long join" procedure is subsequently applied to connect distant fragments. Finally, annotations are exported into GFF3 or gameXML files.
Versions and Availability
Module Names for repet on philip
| Machine | Version | Module Name |
|---|---|---|
| philip | 2.2 | repet/2.2 |
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
Shells
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
/bin/tcsh
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
Default Setup
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
The command
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Managing Modules
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
Module is currently available only on SuperMIC.
Resources
- For additional information, see the text files in: /usr/local/packages/bioinformatics/REPET/2.0/doc (as of the time this was written).
Last modified: August 21 2017 10:47:37.